org.xmlcml.cml
Interface AbstractAtom

All Known Subinterfaces:

Atom, AtomArray

All Known Implementing Classes:

AbstractAtomImpl

public interface AbstractAtom

extends AbstractBuiltinContainer, HasCount

Field Summary

static int	ATOM_BUILTIN_COUNT
static int	ATOM_FLOATVAL_COUNT
static int	ATOM_FLOATVAL_END
static int	ATOM_FLOATVAL_START
static int	ATOM_ID
static int	ATOM_INTEGERVAL_COUNT
static int	ATOM_INTEGERVAL_END
static int	ATOM_INTEGERVAL_START
static int	ATOM_PARITY_FLOAT
static int	ATOM_PARITY_INT
static int	ATOM_STRINGVAL_COUNT
static int	ATOM_STRINGVAL_END
static int	ATOM_STRINGVAL_START
static int	ELEMENT_TYPE
static int	FORMAL_CHARGE_FLOAT
static int	FORMAL_CHARGE_INT
static int	HYDROGEN_COUNT_FLOAT
static int	HYDROGEN_COUNT_INT
static int	ISOTOPE_FLOAT
static int	ISOTOPE_INT
static int	NON_HYDROGEN_COUNT_FLOAT
static int	NON_HYDROGEN_COUNT_INT
static int	OCCUPANCY
static int	RESIDUE_ID
static int	RESIDUE_TYPE
static java.lang.String[]	SMILESATOMS these are the only allowed atoms in SMILES that can be outside [...]
static int	SP
static int	SP2
static int	SP3
static java.lang.String[]	spTypeStrings
static int[]	valences
static int	X2
static int	X3
static int	XFRACT
static int	Y2
static int	Y3
static int	YFRACT
static int	Z3
static int	ZFRACT

Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

NONUNIQUE, UNIQUE

Fields inherited from interface org.xmlcml.cml.HasCount

COUNT

Fields inherited from interface org.xmlcml.cml.CMLBase

ANGLE, ATOM, ATOMARRAY, BOND, BONDARRAY, BUILTIN, CML, CRYSTAL, ELECTRON, ELEMENT_COUNT, ELEMENT_NAMES, EXECUTE, FEATURE, FLOAT, FLOAT_TYPE, FLOATARRAY, FLOATMATRIX, FORMULA, INTEGER, INTEGER_TYPE, INTEGERARRAY, LINK, LIST, MOLECULE, PACKAGE_NAME, REACTION, SEQUENCE, STRING, STRING_TYPE, STRINGARRAY, TORSION, UNK, UNK_ELEM, UNKNOWN

Fields inherited from interface uk.co.demon.ursus.dom.PMRElement

CLASSNAME, LOCAL, QUALIFIED, UNIVERSAL

Fields inherited from interface org.xmlcml.cml.HasTitle

TITLE

Fields inherited from interface org.xmlcml.cml.HasDictRef

DICTREF

Fields inherited from interface org.xmlcml.cml.HasId

ID

Fields inherited from interface org.xmlcml.cml.HasConvention

CONVENTION

Fields inherited from interface uk.co.demon.ursus.dom.PMRNode

ATTRIBUTES, CONTENT, ELEMENTNAME, IDLIST, NESTED, NESTEDATTS, PACKAGENAME, PRETTY, SPLITFILES, STYLE, TAGGED, UNTAGGED, WHITESPACE, XMLCONTENT

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Method Summary

double	getCount()
void	setCount(double count)

Methods inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinCount, getBuiltinVal, getNonBuiltinVal, setBuiltinVal, setNonBuiltinVal

Methods inherited from interface org.xmlcml.cml.HasCount

updateDOMHasCount

Methods inherited from interface org.xmlcml.cml.CMLBase

addValidity, debug, isValid, processDOM, updateDOM

Methods inherited from interface uk.co.demon.ursus.dom.PMRElement

appendTo, getValidity, processDescendants, setProcessFlag, setTagName

Methods inherited from interface org.xmlcml.cml.HasTitle

getTitle, setTitle, updateDOMHasTitle

Methods inherited from interface org.xmlcml.cml.HasDictRef

getDictRef, setDictRef, updateDOMHasDictRef

Methods inherited from interface org.xmlcml.cml.HasId

getId, setId, updateDOMHasId

Methods inherited from interface org.xmlcml.cml.HasConvention

getConventionName, setConventionName, updateDOMHasConvention

Methods inherited from interface org.w3c.dom.Element

getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getElementsByTagName, getElementsByTagNameNS, getTagName, hasAttribute, hasAttributeNS, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS

Field Detail

ATOM_FLOATVAL_START

public static final int ATOM_FLOATVAL_START

X2

public static final int X2

Y2

public static final int Y2

X3

public static final int X3

Y3

public static final int Y3

Z3

public static final int Z3

XFRACT

public static final int XFRACT

YFRACT

public static final int YFRACT

ZFRACT

public static final int ZFRACT

OCCUPANCY

public static final int OCCUPANCY

ISOTOPE_FLOAT

public static final int ISOTOPE_FLOAT

FORMAL_CHARGE_FLOAT

public static final int FORMAL_CHARGE_FLOAT

HYDROGEN_COUNT_FLOAT

public static final int HYDROGEN_COUNT_FLOAT

NON_HYDROGEN_COUNT_FLOAT

public static final int NON_HYDROGEN_COUNT_FLOAT

ATOM_PARITY_FLOAT

public static final int ATOM_PARITY_FLOAT

ATOM_FLOATVAL_END

public static final int ATOM_FLOATVAL_END

ATOM_FLOATVAL_COUNT

public static final int ATOM_FLOATVAL_COUNT

ATOM_INTEGERVAL_START

public static final int ATOM_INTEGERVAL_START

ISOTOPE_INT

public static final int ISOTOPE_INT

FORMAL_CHARGE_INT

public static final int FORMAL_CHARGE_INT

HYDROGEN_COUNT_INT

public static final int HYDROGEN_COUNT_INT

NON_HYDROGEN_COUNT_INT

public static final int NON_HYDROGEN_COUNT_INT

ATOM_PARITY_INT

public static final int ATOM_PARITY_INT

ATOM_INTEGERVAL_END

public static final int ATOM_INTEGERVAL_END

ATOM_INTEGERVAL_COUNT

public static final int ATOM_INTEGERVAL_COUNT

ATOM_STRINGVAL_START

public static final int ATOM_STRINGVAL_START

ELEMENT_TYPE

public static final int ELEMENT_TYPE

ATOM_ID

public static final int ATOM_ID

RESIDUE_TYPE

public static final int RESIDUE_TYPE

RESIDUE_ID

public static final int RESIDUE_ID

ATOM_STRINGVAL_END

public static final int ATOM_STRINGVAL_END

ATOM_STRINGVAL_COUNT

public static final int ATOM_STRINGVAL_COUNT

ATOM_BUILTIN_COUNT

public static final int ATOM_BUILTIN_COUNT

SMILESATOMS

public static final java.lang.String[] SMILESATOMS

these are the only allowed atoms in SMILES that can be outside [...]

valences

public static final int[] valences

SP3

public static final int SP3

SP2

public static final int SP2

SP

public static final int SP

spTypeStrings

public static final java.lang.String[] spTypeStrings

Method Detail

setCount

public void setCount(double count)

Specified by:

setCount in interface HasCount

getCount

public double getCount()

Specified by:

getCount in interface HasCount